No matter what I do, I always seem to end up with windows on top of each other while working on my Mac. Often when I need to drag a file from one window to another (e.g. from Finder to an FTP program), I have to arrange the windows so that I can see parts of each. Then, I can do the drag and drop. I recently found a better way through experimentation. After you begin to drag a file, you can press CMD+Tab with your other hand. This brings up the app switcher. You can either point the dragged file at the destination app or use the hand on the keyboard to tab to the app.
Either way, this is a much faster way to bring the destination app into focus. It makes dragging and dropping much more efficient regardless of how many windows you have open.